Windows 10 deleted the Windows folder in another harddrive

pinoy

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I have Windows 10 installed on SSD(1) which is connected to sata port 1. I got a new SSD(2) and connected it to sata port 3. I disconnect SSD 1 from port 1 before installing Windows 10 on SSD 2. I got Windows all setup on SSD 2 and rebooted several times to make sure everything is fine. I then proceeded to reconnect SSD 1 on sata port 1. The computer boots SSD 1 and everything looks fine. When I go to Explorer I noticed SSD 2 is completely empty. Somehow the entire Windows installation on SSD 2 is being deleted by the first Windows installation. I have repeated this process three times and each time the same result. Why is Windows 10 deleting the Windows installation in another drive? This is just ridiculous.
 
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B00nie

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I have Windows 10 installed on SSD(1) which is connected to sata port 1. I got a new SSD(2) and connected it to sata port 3. I disconnect SSD 1 from port 1 before installing Windows 10 on SSD 2. I got Windows all setup on SSD 2 and rebooted several times to make sure everything is fine. I then proceeded to reconnect SSD 1 on sata port 1. The computer boots SSD 1 and everythign looks fine. When I go to Explorer I noticed SSD 1 is completely empty. Somehow the entire Windows installation on SSD 2 is being deleted by the first Windows installation. I have repeated this process three times and each time the same result. Why is Windows 10 deleting the Windows installation in another drive? This is just ridiculous.
How can it boot from SSD1 if SSD1 is empty.
 

GotNoRice

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I put other drives with Windows 10 installs on them into my main computer all the time (at least once per week) in order to do backups or copy the partition to another drive. I've never once had Windows 10 delete anything on another drive automatically, regardless of if the other drive has a Windows install on it or not.

When you boot using SSD1 again, after doing the install on SSD2, what does it show in Disk Management? Does it show any partitions on SSD2? Are any of them assigned a drive letter?
 
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pinoy

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Typo fixed. I've reinstalled Windows 10 on SSD 2 three times with almost similar catastrophic results. SSD 2 does show in Disk Management and shows only as Primary Partition and Active. The capacity is 465 GB but the free space is only 441 GB and the drive appears empty. Clearly the missing space is still occupied by the missing Windows installation but it's not visible or accessible. Interestingly, when Windows was still booting on SSD 2, Disk Management showed the drive also as System, Boot, Page File, Crash Dump.

I wonder if it's a drive firmware issue. SSD 1 is Samsung 870 EVO and SSD 2 is Crucial MX500. I'm about to swap the drives and reinstall Windows to both and see if the problem repeats.
 

ninjadoc

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I had Windows 10 disable the boot sector on a second Windows 10 drive. The drive is not seen in boot manager but it is seen in Disk Management. I can not activate the partition in Disk management and I can not activate the boot partition from an elevated (administrative) command pro,pt. I tried booting from the install disk and repair the disk but repair doesn't even recognize the drive as a disk that has Windows 10 installed. I also tried to activate the drive going through the command disk on advanced repair. I'm unable to get that disk to be recognized by boot manager. I also can't change the disk to the boot disk because of the way MSI makes their bios. If I disable boot manager in the bios I still can't make the disk bootable.

It is not the same problem as pinoy's but it does demonstrate that Windows 10 will change other drives with OS's installed. It is a weird issue but it seems to be one of a myriad of Windows 10 features/quirks that I find troublesome.
 

pendragon1

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what are you trying to do, dual boot? its probably the way the second install is setting up the drive, maybe mbr vs gpt or that both are marked as active boot drives. if you are trying to dual boot. make a back up of the first drive, then leave both connected and install to drive 2. windows will automatically setup the dual boot.
 

Chuklr

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I have Windows 10 installed on SSD(1) which is connected to sata port 1. I got a new SSD(2) and connected it to sata port 3. I disconnect SSD 1 from port 1 before installing Windows 10 on SSD 2. I got Windows all setup on SSD 2 and rebooted several times to make sure everything is fine. I then proceeded to reconnect SSD 1 on sata port 1. The computer boots SSD 1 and everything looks fine. When I go to Explorer I noticed SSD 2 is completely empty. Somehow the entire Windows installation on SSD 2 is being deleted by the first Windows installation. I have repeated this process three times and each time the same result. Why is Windows 10 deleting the Windows installation in another drive? This is just ridiculous.
Did you activate the Windows 10 installation with a Product Key different from the SSD1 Windows 10 installation, or did you just find that SSD2 installation automatically activated?
 

ninjadoc

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what are you trying to do, dual boot? its probably the way the second install is setting up the drive, maybe mbr vs gpt or that both are marked as active boot drives. if you are trying to dual boot. make a back up of the first drive, then leave both connected and install to drive 2. windows will automatically setup the dual boot.
If they are both marked as boot drives wouldn't they both show up in boot manager?
Both should be GPT but I would have to check - why would that matter?
 

pendragon1

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If they are both marked as boot drives wouldn't they both show up in boot manager?
Both should be GPT but I would have to check - why would that matter?
no, because the first drive was disconnected so the second doesnt know it exists.
 

B00nie

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If the OP had any other drive connected during the experiments it's possible that the boot manager was written on that and then overwritten when installing the second installation. I wonder why the OP is seeing the trouble with two Windows installs. Most likely he should install Windows for whatever reason he needs it and then install linux for dual boot. Linux is smart enough to handle the boot situation, Windows isn't.
 

pendragon1

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If the OP had any other drive connected during the experiments it's possible that the boot manager was written on that and then overwritten when installing the second installation. I wonder why the OP is seeing the trouble with two Windows installs. Most likely he should install Windows for whatever reason he needs it and then install linux for dual boot. Linux is smart enough to handle the boot situation, Windows isn't.
read the op. he states he is disconnecting drives during setup.
edit: and yes it is. you dont use it, as youve stated, so dont make assumptions.
 

B00nie

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read the op. he states he is disconnecting drives during setup.
edit: and yes it is. you dont use it, as youve stated, so dont make assumptions.
He said he was disconnecting THOSE drives, not all of them. Which I suspect is the root of his problems.
 

pinoy

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OK, after installing Windows 10 eight times last night I am no where close to coming up with a definite cause of the problem and I'm leaning more towards a SSD incompatibility with my old Asus M4A88TD-M/USB3 motherboard. Once again I'm installing Windows 10 with only one drive attached at a time. On my last test I put SSD 2 on sata port 1 and installed Windows 10. I disconnected that and I put SSD 1 on sata port 3 and installed Windows 10. Everything good so far after multiple reboots. Windows was booting up fine on each drive by themselves. I now connected both drives, SSD 2 still on port 1 and SSD 1 on port 3. Bios defaults to loading Windows 10 on SSD2 and does its circle animation and then it popped an error screen similar to the one shown below but it was green and not blue. I was not able to reproduce the screen to take a picture of it as it was quick. Windows eventually loaded completely and appeared normal. The Windows installed folders on SSD 1 appeared to be still intact while in previous tests it was already gone at this point. I go to Windows Maintenance and it showed it want's to reboot and do a chkdsk on SSD1. Oh boy. It did the reboot and chkdsk twice. Windows loaded and now SSD 1 is visible in Explorer but inaccessible and does show up in Disk Management as Healthy. Event Viewer shows multiple errors about corruption of the MFT table. Each reboot it wanted to keep doing chkdsk on SSD 1. I gave up at this point. There are too many variables at play and the behaviour is not quite the same each time but the end result is a non working Windows installation on whichever SSD is on port 3. The problem could be Windows 10, motherboard, SSD firmware. I bet it works fine if I have all the drives connected and install Windows on each drive. I'm just sick of installing Windows at this point.

ERROR.jpg
 

pendragon1

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like i said: they dont know each other are there, its messing it up.
IF you have any other drives disconnect them.
install both drives, boot off installer, erase all partitions, install on #1, complete install.
boot off installer, install on #2. you should now have two bootable installs (edit: and a windows boot menu). boot #2, complete install.
boot #1, use bcdedit to rename the boot menu names if you want.
 
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ninjadoc

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I'm confused on what your goal is? Where you trying a dual boot or trying to reconnect the old windows installation to copy files to the new installation? Or was this one of those weird things that occurred when you tried to clone a drive and everything went to hell?

I've tried that and the directories just disappear. I've also reconnected the old boot drive to the previous PC, copied the files to another hard drive, then disconnected that hard drive from that PC and connected it to the new PC. As I mentioned in another thread hot swapping is a known issue with Windows 10 so it didn't recognize the drive so I had to reboot. I had copied the documents and photo directory from the old PC to the drive with administrative privileges. I could not access those directories on the new PC even when I answered "yes" to Windows asking if I wanted access to the directory. That directory then promptly disappeared. I've also seen the above screen before.
 

pinoy

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I have four other HDD with different version of Windows. I regularly swap drives depending on what old software I want to run. I like to have each drive have their own boot files so I don't make a mistake of removing a boot drive and then rendering the computer unbootable. My concern now is if this problem is limited to the combination of SSD drives I was using and a Windows 10 bug?. I would hate to plug in one of my drives and then the contents get deleted out of nowhere. This is my first experience with SSD and have never had problems with HDD.
 
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ninjadoc

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My suspicion is it is a Windows 10 bug. I read about issues with hot swap and with Windows 10 drivers. Try the same experiment with hard drives. I’m curious about what happens.

Being paranoid I would not hookup one of my other OS’s and any drive with Win 10 after what you’ve told me.
 

Nobu

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If you boot a linux distro after windows clobbers your drive, can you still access the data or does it give errors trying to mount it?
 

B00nie

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I'm suspecting this might be simply a privilege issue, perhaps Windows will hide the folders if the user of the "other" OS has no privileges to it. So the data is there, Windows just refuses to show it. Given the direction of taking away control of the user Windows has had, it wouldn't surprise me one bit. This kind of functionality would make it very convenient for Microsoft to place hidden files and folders anywhere they like in the system.
 

pinoy

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I'm heavily leaning to a Windows 10 bug regarding how it deals with multiple drives having their own boot files in combination with my particular hardware. I tried the experiment on a different computer this time. One SSD on port 1 and a HDD on port 2. The HDD had Windows 10 on it and when I installed Windows 10 on the SSD it set up a dual boot menu. The installation kept the boot files located on the HDD and the SSD was set to load by default. If I disconnect the SSD and boot the computer I get a Recovery blue screen similar to what I posted above, but I'm given the option to load the alternate OS on the HDD. Windows continues to load just fine and nothing ever got deleted or went missing.

On my next test I added a different SSD and installed Windows 10 on that separately. I reconnected the HDD but not the accompanying SSD from the first test. Remember the boot files for dual boot was on the HDD. When I boot off the SSD everything looked fine. Nothing ever got deleted on the HDD. I didn't get any blue screen. The only error I saw was in the Event Viewer complaining about the missing Volume which is probably the disconnected SSD. I was able to get rid of the Error message by modifying the boot files on the HDD using bcdedit to remove the dual boot option.

As you can see totally different behaviour from my first computer.
 

pendragon1

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I'm heavily leaning to a Windows 10 bug regarding how it deals with multiple drives having their own boot files in combination with my particular hardware. I tried the experiment on a different computer this time. One SSD on port 1 and a HDD on port 2. The HDD had Windows 10 on it and when I installed Windows 10 on the SSD it set up a dual boot menu. The installation kept the boot files located on the HDD and the SSD was set to load by default. If I disconnect the SSD and boot the computer I get a Recovery blue screen similar to what I posted above, but I'm given the option to load the alternate OS on the HDD. Windows continues to load just fine and nothing ever got deleted or went missing.

On my next test I added a different SSD and installed Windows 10 on that separately. I reconnected the HDD but not the accompanying SSD from the first test. Remember the boot files for dual boot was on the HDD. When I boot off the SSD everything looked fine. Nothing ever got deleted on the HDD. I didn't get any blue screen. The only error I saw was in the Event Viewer complaining about the missing Volume which is probably the disconnected SSD. I was able to get rid of the Error message by modifying the boot files on the HDD using bcdedit to remove the dual boot option.

As you can see totally different behaviour from my first computer.
thats totally different from what you describe in your op as you created the dual boot, and its files, on the hdd. you can recreate your "problem" by wiping both the hdd and ssd, installing windows on them separately and them combining them. its not the system, its how you are installing.
 

pinoy

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I just read an article from 2017 about Windows Fast Startup and dual boot can cause corruption. Windows 10 has Fast Startup enabled by default. The article said accessing or modifying a drive from a dual boot setup that has Fast Startup enabled may corrupt it. I don't know how accurate the article still is or if it's a bug that's been fixed since 2017. The article said you can't access the Fast Startup drive from another Operating System in a dual boot setup. Well, I certainly can.
 

B00nie

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Why do you keep messing with dual boot when you can virtualize your windows and run easily 10 copies as you like? You're doing it completely wrong right now. Windows has never been able to reliably handle a dual boot system, it can barely stay in one piece with single boot.
 
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